The Antennapedia-type homeobox genes have evolved from three precursors separated early in metazoan evolution

Suboptimal Intermediates Underlie Evolution of the Bicoid Homeodomain

Changes in regulatory networks generate materials for evolution to create phenotypic diversity. For transcription networks, multiple studies have shown that alterations in binding sites of cis-regulatory elements correlate well with the gain or loss of specific features of the body plan. Less is known about alterations in the amino acid sequences of the transcription factors (TFs) that bind these elements. Here we study the evolution of Bicoid (Bcd), a homeodomain (HD) protein that is critical for anterior embryo patterning in Drosophila. The ancestor of Bcd (AncBcd) emerged after a duplication of a Zerknullt (Zen)-like ancestral protein (AncZB) in a suborder of flies. AncBcd diverged from AncZB, gaining novel transcriptional and translational activities. We focus on the evolution of the HD of AncBcd, which binds to DNA and RNA, and is comprised of four subdomains: an N-terminal arm (NT) and three helices; H1, H2, and Recognition Helix (RH). Using chimeras of subdomains and gene rescue assays in Drosophila, we show that robust patterning activity of the Bcd HD (high frequency rescue to adulthood) is achieved only when amino acid substitutions in three separate subdomains (NT, H1, and RH) are combined. Other combinations of subdomains also yield full rescue, but with lower penetrance, suggesting alternative suboptimal activities. Our results suggest a multistep pathway for the evolution of the Bcd HD that involved intermediate HD sequences with suboptimal activities, which constrained and enabled further evolutionary changes. They also demonstrate critical epistatic forces that contribute to the robust function of a DNA-binding domain.

The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution

Neo-Darwinian explanations of organic evolution have settled on mutation as the principal factor in producing evolutionary novelty. Mechanistic characterizations have been also biased by the classic dogma of molecular biology, where only proteins regulate gene expression. This together with the rearrangement of genetic information, in terms of genes and chromosomes, was considered the cornerstone of evolution at the level of natural populations. This predominant view excluded both alternative explanations and phenomenologies that did not fit its paradigm. With the discovery of non-coding RNAs (ncRNAs) and their role in the control of genetic expression, new mechanisms arose providing heuristic power to complementary explanations to evolutionary processes overwhelmed by mainstream genocentric views. Viruses, epimutation, paramutation, splicing, and RNA editing have been revealed as paramount functions in genetic variations, phenotypic plasticity, and diversity. This article discusses how current epigenetic advances on ncRNAs have changed the vision of the mechanisms that generate variation, how organism-environment interaction can no longer be underestimated as a driver of organic evolution, and how it is now part of the transgenerational inheritance and evolution of species.

Looking Beyond the Genes: The Interplay Between Signaling Pathways and Mechanics in the Shaping and Diversification of Epithelial Tissues

The core of Evo-Devo lies in the intuition that the way tissues grow during embryonic development, the way they sustain their structure and function throughout lifetime, and the way they evolve are closely linked. Epithelial tissues are ubiquitous in metazoans, covering the gut and internal branched organs, as well as the skin and its derivatives (ie, teeth). Here, we discuss in vitro, in vivo, and in silico studies on epithelial tissues to illustrate the conserved, dynamical, and complex aspects of their development. We then explore the implications of the dynamical and nonlinear nature of development on the evolution of their size and shape at the phenotypic and genetic levels. In rare cases, when the interplay between signaling and mechanics is well understood at the cell level, it is becoming clear that the structure of development leads to covariation of characters, an integration which in turn provides some predictable structure to evolutionary changes. We suggest that such nonlinear systems are prone to genetic drift, cryptic genetic variation, and context-dependent mutational effects. We argue that experimental and theoretical studies at the cell level are critical to our understanding of the phenotypic and genetic evolution of epithelial tissues, including carcinomas.

Distinct molecular strategies for Hox-mediated limb suppression in Drosophila: from cooperativity to dispensability/antagonism in TALE partnership

The emergence following gene duplication of a large repertoire of Hox paralogue proteins underlies the importance taken by Hox proteins in controlling animal body plans in development and evolution. Sequence divergence of paralogous proteins accounts for functional specialization, promoting axial morphological diversification in bilaterian animals. Yet functionally specialized paralogous Hox proteins also continue performing ancient common functions. In this study, we investigate how highly divergent Hox proteins perform an identical function. This was achieved by comparing in Drosophila the mode of limb suppression by the central (Ultrabithorax and AbdominalA) and posterior class (AbdominalB) Hox proteins. Results highlight that Hox-mediated limb suppression relies on distinct modes of DNA binding and a distinct use of TALE cofactors. Control of common functions by divergent Hox proteins, at least in the case studied, relies on evolving novel molecular properties. Thus, changes in protein sequences not only provide the driving force for functional specialization of Hox paralogue proteins, but also provide means to perform common ancient functions in distinct ways.

The origin of patterning systems in bilateria-insights from the Hox and ParaHox genes in Acoelomorpha

Hox and ParaHox genes constitute two families of developmental regulators that pattern the Anterior–Posterior body axis in all bilaterians. The members of these two groups of genes are usually arranged in genomic clusters and work in a coordinated fashion, both in space and in time. While the mechanistic aspects of their action are relatively well known, it is still unclear how these systems evolved. For instance, we still need a proper model of how the Hox and ParaHox clusters were assembled over time. This problem is due to the shortage of information on gene complements for many taxa (mainly basal metazoans) and the lack of a consensus phylogenetic model of animal relationships to which we can relate our new findings. Recently, several studies have shown that the Acoelomorpha most probably represent the first offshoot of the Bilateria. This finding has prompted us, and others, to study the Hox and ParaHox complements in these animals, as well as their activity during development. In this review, we analyze how the current knowledge of Hox and ParaHox genes in the Acoelomorpha is shaping our view of bilaterian evolution.

Evolution of Hox complexes

Recent years have seen a plethora of ideas and hypotheses, and lots of debate, about the origin and evolution of the Hox gene cluster. Here I will attempt to summarize these hypotheses, identify their strengths and weaknesses and highlight the types of new data that may lead to further resolution of the competing ideas. The major theme is that Hox genes originated very early in animal evolution and extensive independent duplications occurred in major lineages. Duplications however have not been the only route to change in the composition and structure of the Hox cluster, as extensive gene losses have occurred as well. Indeed it is gene loss that is one of the main obstacles in our understanding of the origin and evolution of Hox clusters. Matters should be improved with wider taxon sampling along with a clearer understanding of how duplicated genes evolve.

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome

The living coelacanth is a lobe-finned fish that represents an early evolutionary departure from the lineage that led to land vertebrates, and is of extreme interest scientifically. It has changed very little in appearance from fossilized coelacanths of the Cretaceous (150 to 65 million years ago), and is often referred to as a "living fossil." An important general question is whether long-term stasis in morphological evolution is associated with stasis in genome evolution. To this end we have used targeted genome sequencing for acquiring 1,612,752 bp of high quality finished sequence encompassing the four HOX clusters of the Indonesian coelacanth Latimeria menadoensis. Detailed analyses were carried out on genomic structure, gene and repeat contents, conserved noncoding regions, and relative rates of sequence evolution in both coding and noncoding tracts. Our results demonstrate conclusively that the coelacanth HOX clusters are evolving comparatively slowly and that this taxon should serve as a viable outgroup for interpretation of the genomes of tetrapod species.

PCR survey of hox genes in the goldfish Carassius auratus auratus

A tetraploidization event took place in the cyprinid lineage leading to goldfishes about 15 million years ago. A PCR survey for Hox genes in the goldfish Carassius auratus auratus (Actinopterygii: Cyprinidae) was performed to assess the consequences of this genome duplication. Not surprisingly, the genomic organization of the Hox gene clusters of goldfish is similar to that of the closely related zebrafish (Danio rerio). However, the goldfish exhibits a much larger number of recent pseudogenes, which are characterized by indels. These findings are consistent with the hypothesis that dosage effects cause selection pressure to rapidly silence crucial developmental regulators after a tetraploidization event.

Common functions of central and posterior Hox genes for the repression of head in the trunk of Drosophila

Hox genes are localised in complexes, encode conserved homeodomain transcription factors and have mostly been studied for their specialised functions: the formation of distinct structures along the anteroposterior axis. They probably derived via duplication followed by divergence, from a unique gene, suggesting that Hox genes may have retained a common function. The comparison of their homeodomain sequences groups Hox proteins into Anterior, Central and Posterior classes, reflecting their expression patterns in the head, trunk and tail, respectively. However, functional data supporting this classification are rare. Here, we re-examine a common activity of Hox genes in Drosophila: the repression of head in the trunk. First, we show that central and posterior Hox genes prevent the expression of the head specific gene optix in the trunk, providing a functional basis for the classification. Loss-of-function mutations of optix affect embryonic head development, whereas ectopic Optix expression strongly perturbs trunk development. Second, we demonstrate that the non-Hox genes teashirt, extradenticle and homothorax are required for the repression of optix and that Wingless signalling and Engrailed contribute to this repression. We propose that an evolutionary early function of Hox genes was to modify primitive head morphology with novel functions specialising the trunk appearing later on.

Duplicated Hox genes in the spider Cupiennius salei

Background

Hox genes are expressed in specific domains along the anterior posterior body axis and define the regional identity. In most animals these genes are organized in a single cluster in the genome and the order of the genes in the cluster is correlated with the anterior to posterior expression of the genes in the embryo. The conserved order of the various Hox gene orthologs in the cluster among most bilaterians implies that such a Hox cluster was present in their last common ancestor. Vertebrates are the only metazoans so far that have been shown to contain duplicated Hox clusters, while all other bilaterians seem to possess only a single cluster.

Results

We here show that at least three Hox genes of the spider Cupiennius salei are present as two copies in this spider. In addition to the previously described duplicated Ultrabithorax gene, we here present sequence and expression data of a second Deformed gene, and of two Sex comb reduced genes. In addition, we describe the sequence and expression of the Cupiennius proboscipedia gene. The spider Cupiennius salei is the first chelicerate for which orthologs of all ten classes of arthropod Hox genes have been described. The posterior expression boundary of all anterior Hox genes is at the tagma border of the prosoma and opisthosoma, while the posterior boundary of the posterior Hox genes is at the posterior end of the embryo.

Conclusion

The presence of at least three duplicated Hox genes points to a major duplication event in the lineage to this spider, perhaps even of the complete Hox cluster as has taken place in the lineage to the vertebrates. The combined data of all Cupiennius Hox genes reveal the existence of two distinct posterior expression boundaries that correspond to morphological tagmata boundaries.

Pre-bilaterian origins of the Hox cluster and the Hox code: evidence from the sea anemone, Nematostella vectensis

BACKGROUND

Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone Nematostella vectensis challenge recent claims that the Hox code is a bilaterian invention and that no "true" Hox genes exist in the phylum Cnidaria.

METHODOLOGY/PRINCIPAL FINDINGS

Phylogenetic analyses of 18 Hox-related genes from Nematostella identify putative Hox1, Hox2, and Hox9+ genes. Statistical comparisons among competing hypotheses bolster these findings, including an explicit consideration of the gene losses implied by alternate topologies. In situ hybridization studies of 20 Hox-related genes reveal that multiple Hox genes are expressed in distinct regions along the primary body axis, supporting the existence of a pre-bilaterian Hox code. Additionally, several Hox genes are expressed in nested domains along the secondary body axis, suggesting a role in "dorsoventral" patterning.

CONCLUSIONS/SIGNIFICANCE

A cluster of anterior and posterior Hox genes, as well as ParaHox cluster of genes evolved prior to the cnidarian-bilaterian split. There is evidence to suggest that these clusters were formed from a series of tandem gene duplication events and played a role in patterning both the primary and secondary body axes in a bilaterally symmetrical common ancestor. Cnidarians and bilaterians shared a common ancestor some 570 to 700 million years ago, and as such, are derived from a common body plan. Our work reveals several conserved genetic components that are found in both of these diverse lineages. This finding is consistent with the hypothesis that a set of developmental rules established in the common ancestor of cnidarians and bilaterians is still at work today.

Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes

We isolated BAC clones that cover the entire hox gene loci in the medaka fish Oryzias latipes. The BAC clones were characterized by the Southern hybridization with many hox gene probes isolated in our previous study and by PCR using primers designed for selective amplification of respective hox genes. Then, the BAC clones have been subjected to shotgun sequencing. The results revealed the organization of the entire hox gene loci. Forty-six hox genes in total are encoded in seven clusters as follows: 10 hox genes in Aa cluster; 5 in Ab; 9 in Ba; 4 in Bb; 10 in Ca; 6 in Da; and 2 in Db. Together with the information on the hox gene loci registered in the Fugu genome database and in the Danio genome database, the physical maps of three fish genomes were constructed and compared one another. Not only numbers of hox genes but also the distances between the neighboring hox genes are highly similar between medaka and fugu. As for six clusters, Aa, Ab, Ba, Bb, Ca and Da that are commonly present in the three fishes, only few or no differences were found in each cluster. Thus, the hox gene sets should have been well conserved once they had been established in respective species.

The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts

The Hox gene complement of zebrafish, medaka, and fugu differs from that of other gnathostome vertebrates. These fishes have seven to eight Hox clusters compared to the four Hox clusters described in sarcopterygians and shark. The clusters in different teleost lineages are orthologous, implying that a "fish-specific" Hox cluster duplication has occurred in the stem lineage leading to the most recent common ancestor of zebrafish and fugu. The timing of this event, however, is unknown. To address this question, we sequenced four Hox genes from taxa representing basal actinopterygian and teleost lineages and compared them to known sequences from shark, coelacanth, zebrafish, and other teleosts. The resulting gene genealogies suggest that the fish-specific Hox cluster duplication occurred coincident with the origin of crown group teleosts. In addition, we obtained evidence for an independent Hox cluster duplication in the sturgeon lineage (Acipenseriformes). Finally, results from HoxA11 suggest that duplicated Hox genes have experienced diversifying selection immediately after the duplication event. Taken together, these results support the notion that the duplicated Hox genes of teleosts were causally relevant to adaptive evolution during the initial teleost radiation.

Evolution of microRNAs located withinHox gene clusters

MicroRNAs (miRNAs) form an abundant class of non-coding RNA genes that have an important function in post-transcriptional gene regulation and in particular modulate the expression of developmentally important transcription factors including Hox genes. Two families of microRNAs are genomically located in intergenic regions in the Hox clusters of vertebrates. Here we describe their evolution in detail. We show that the micro RNAs closely follow the patterns of protein evolution in the Hox clusters, which is characterized by cluster duplications followed by differential gene loss.

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications

Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. Since these elements are subject to stabilizing selection they evolve much more slowly than adjacent non-functional DNA. These so-called phylogenetic footprints can be detected by comparison of the sequences surrounding orthologous genes in different species. Therefore the loss of phylogenetic footprints as well as the acquisition of conserved non-coding sequences in some lineages, but not in others, can provide evidence for the evolutionary modification of cis-regulatory elements. We introduce here a statistical model of footprint evolution that allows us to estimate the loss of sequence conservation that can be attributed to gene loss and other structural reasons. This approach to studying the pattern of cis-regulatory element evolution, however, requires the comparison of relatively long sequences from many species. We have therefore developed an efficient software tool for the identification of corresponding footprints in long sequences from multiple species. We apply this novel method to the published sequences of HoxA clusters of shark, human, and the duplicated zebrafish and Takifugu clusters as well as the published HoxB cluster sequences. We find that there is a massive loss of sequence conservation in the intergenic region of the HoxA clusters, consistent with the finding in [Chiu et al., PNAS 99 (2002) 5492]. The loss of conservation after cluster duplication is more extensive than expected from structural reasons. This suggests that binding site turnover and/or adaptive modification may also contribute to the loss of sequence conservation.

The duplication of the Hox gene clusters in teleost fishes

Higher teleost fishes, including zebrafish and fugu, have duplicated their Hox genes relative to the gene inventory of other gnathostome lineages. The most widely accepted theory contends that the duplicate Hox clusters orginated synchronously during a single genome duplication event in the early history of ray-finned fishes. In this contribution we collect and re-evaluate all publicly available sequence information. In particular, we show that the short Hox gene fragments from published PCR surveys of the killifish Fundulus heteroclitus, the medaka Oryzias latipes and the goldfish Carassius auratus can be used to determine with little ambiguity not only their paralog group but also their membership in a particular cluster.Together with a survey of the genomic sequence data from the pufferfish Tetraodon nigroviridis we show that at least percomorpha, and possibly all eutelosts, share a system of 7 or 8 orthologous Hox gene clusters. There is little doubt about the orthology of the two teleost duplicates of the HoxA and HoxB clusters. A careful analysis of both the coding sequence of Hox genes and of conserved non-coding sequences provides additional support for the "duplication early" hypothesis that the Hox clusters in teleosts are derived from eight ancestral clusters by means of subsequent gene loss; the data remain ambiguous, however, in particular for the HoxC clusters.Assuming the "duplication early" hypothesis we use the new evidence on the Hox gene complements to determine the phylogenetic positions of gene-loss events in the wake of the cluster duplication. Surprisingly, we find that the resolution of redundancy seems to be a slow process that is still ongoing. A few suggestions on which additional sequence data would be most informative for resolving the history of the teleostean Hox genes are discussed.

Exclusion of repetitive DNA elements from gnathostomeHox clusters

Despite their homology and analogous function, the Hox gene clusters of vertebrates and invertebrates are subject to different constraints on their structural organization. This is demonstrated by a drastically different distribution of repetitive DNA elements in the Hox cluster regions. While gnathostomes have a strong tendency to exclude repetitive DNA elements from the inside of their Hox clusters, no such trend can be detected in the Hox gene clusters of protostomes. Repeats "invade" the gnathostome Hox clusters from the 5' and 3' ends while the core of the clusters remains virtually free of repetitive DNA. This invasion appears to be correlated with relaxed constraints associated with gene loss after cluster duplications.

Temporal transcription of two antennapedia class homeobox genes in the marine copepod Calanus helgolandicus

DNA sequence information has been obtained for 2 genes implicated in playing critical roles in copepod development. The first ( Cal-antp) was obtained by screening a Calanus helgolandicus genomic library. It shows homology to Antennapedia homeobox genes from a number of organisms including the centipede (76.8% over 250 bp) and the brine shrimp (75.5% over 220 bp). A second sequence (Hox 12) was obtained through reverse transcription polymerase chain reaction (PCR) of a solid-phase cDNA library constructed from Calanus eggs, and subsequent inverse PCR using a genomic DNA template. The Hox 12 sequence is homologous to the Antennapedia class of genes and shares homology with the chicken HoxB3 gene (71% over 187 bp) and with the fruit fly Sex Combs Reduced ( Scr) homeotic gene (66% identity over 223 bp). Using sequence data from Cal-Antp and Hox 12, specific primers were designed to investigate the temporal expression of these genes by PCR analysis of 10 stage-specific cDNA libraries.

Independent Hox-cluster duplications in lampreys

The analysis of the publicly available Hox gene sequences from the sea lamprey Petromyzon marinus provides evidence that the Hox clusters in lampreys and other vertebrate species arose from independent duplications. In particular, our analysis supports the hypothesis that the last common ancestor of agnathans and gnathostomes had only a single Hox cluster which was subsequently duplicated independently in the two lineages.

Hox and paraHox genes from the anthozoan Parazoanthus parasiticus

We surveyed the genome of the Caribbean zoanthid Parazoanthus parasiticus for Hox and paraHox genes, and examined gene expression patterns for sequences we uncovered. Two Hox genes and three paraHox genes were identified in our surveys. The Hox genes belong to anterior and posterior classes. In phylogenetic analyses, the anterior Hox sequence formed an anthozoan-specific cluster that appears to be a second class of cnidarian anterior Hox gene. The presence of an anterior Gsx-like paraHox gene supports the hypothesis that duplication of a protoHox gene family preceded the divergence of the Cnidaria and bilaterians. The presence of two Mox class paraHox genes in P. parasiticus deserves further attention. Expression analysis using RT-PCR, indicated that one Mox gene and the anterior paraHox gene are not expressed in adult tissue, whereas the other three sequences are expressed in both dividing and unitary polyps. Dividing polyps showed slightly lower Ppox1 (i.e., Mox) expression levels. Our data add to the number of published anthozoan sequences, and provide additional detail concerning the evolutionary significance of cnidarian Hox and paraHox genes.

Genesis and evolution of the Evx and Mox genes and the extended Hox and ParaHox gene clusters

BACKGROUND

Hox and ParaHox gene clusters are thought to have resulted from the duplication of a ProtoHox gene cluster early in metazoan evolution. However, the origin and evolution of the other genes belonging to the extended Hox group of homeobox-containing genes, that is, Mox and Evx, remains obscure. We constructed phylogenetic trees with mouse, amphioxus and Drosophila extended Hox and other related Antennapedia-type homeobox gene sequences and analyzed the linkage data available for such genes.

RESULTS

We claim that neither Mox nor Evx is a Hox or ParaHox gene. We propose a scenario that reconciles phylogeny with linkage data, in which an Evx/Mox ancestor gene linked to a ProtoHox cluster was involved in a segmental tandem duplication event that generated an array of all Hox-like genes, referred to as the 'coupled' cluster. A chromosomal breakage within this cluster explains the current composition of the extended Hox cluster (with Evx, Hox and Mox genes) and the ParaHox cluster.

CONCLUSIONS

Most studies dealing with the origin and evolution of Hox and ParaHox clusters have not included the Hox-related genes Mox and Evx. Our phylogenetic analyses and the available linkage data in mammalian genomes support an evolutionary scenario in which an ancestor of Evx and Mox was linked to the ProtoHox cluster, and that a tandem duplication of a large genomic region early in metazoan evolution generated the Hox and ParaHox clusters, plus the cluster-neighbors Evx and Mox. The large 'coupled' Hox-like cluster EvxHox/MoxParaHox was subsequently broken, thus grouping the Mox and Evx genes to the Hox clusters, and isolating the ParaHox cluster.

A source for expression profiling in single preimplantation bovine embryos

Our knowledge of the genes active during normal preimplantation development in cattle is limited, despite the importance for further improvement of fertility and applicability of biotechniques, like in vitro production and embryo transfer. We report on the construction of cDNA libraries as a source for expression profiling in oocytes and single preimplantation cattle embryos. cDNAs were prepared from two unfertilized oocytes, single two-cell, four-cell and eight-cell, morula, and blastocyst stage embryos, respectively. The oocytes, eight-cell, morula, and blastocyst stage embryo-derived cDNAs were ligated to a lambda-based expression vector and these have complexities of 8 x 10(5), 5 x 10(5), 1 x 10(6) and 2 x 10(6) independent clones, respectively. A total of 48 clones were picked and sequenced, 62.5% (30/48) of the sequence were homologous to known transcripts from human and mouse, 18.75% (9/48) to expressed sequence tags (ESTs) of human and mouse origin. Novel sequences were detected at a frequency of 14.58% (7/48). PCR analyses of the embryonic libraries for specific genes revealed transcripts for genes including housekeeping genes (GAPDH and beta-actin), developmental genes (OCT-4, IGF-I receptor and homeodomain sequences) and genes coding for metabolic and protective enzymes (manganese superoxide dismutase, glutamine synthetase, flavin-containing mono-oxygenase, glutamate dehydrogenase, alpha-2-macroglobulin). These cDNA libraries are a valuable resource for the isolation of clones representing genes active at these early developmental stages. The ability to construct cDNA expression libraries from only a few cells will allow gene expression analyses from embryo biopsies and embryos derived by nuclear transfer procedures.

Sequence of the Tribolium castaneum homeotic complex: the region corresponding to the Drosophila melanogaster antennapedia complex

The homeotic selector genes of the red flour beetle, Tribolium castaneum, are located in a single cluster. We have sequenced the region containing the homeotic selector genes required for proper development of the head and anterior thorax, which is the counterpart of the ANTC in Drosophila. This 280-kb interval contains eight homeodomain-encoding genes, including single orthologs of the Drosophila genes labial, proboscipedia, Deformed, Sex combs reduced, fushi tarazu, and Antennapedia, as well as two orthologs of zerknüllt. These genes are all oriented in the same direction, as are the Hox genes of amphioxus, mice, and humans. Although each transcription unit is similar to its Drosophila counterpart in size, the Tribolium genes contain fewer introns (with the exception of the two zerknüllt genes), produce shorter mRNAs, and encode smaller proteins. Unlike the ANTC, this region of the Tribolium HOMC contains no additional genes.

HOX genes in the sepiolid squid Euprymna scolopes: implications for the evolution of complex body plans

Molluscs display a rich diversity of body plans ranging from the wormlike appearance of aplacophorans to the complex body plan of the cephalopods with highly developed sensory organs, a complex central nervous system, and cognitive abilities unrivaled among the invertebrates. The aim of the current study is to define molecular parameters relevant to the developmental evolution of cephalopods by using the sepiolid squid Euprymna scolopes as a model system. Using PCR-based approaches, we identified one anterior, one paralog group 3, five central, and two posterior group Hox genes. The deduced homeodomain sequences of the E. scolopes Hox cluster genes are most similar to known annelid, brachiopod, and nemertean Hox gene homeodomain sequences. Our results are consistent with the presence of a single Hox gene cluster in cephalopods. Our data also corroborate the proposed existence of a differentiated Hox gene cluster in the last common ancestor of Bilaterians. Furthermore, our phylogenetic analysis and in particular the identification of Post-1 and Post-2 homologs support the Lophotrochozoan clade.

Hox gene sequences from the geophilomorph centipede Pachymerium ferrugineum (C. L. Koch, 1835) (Chilopoda: Geophilomorpha: Geophilidae): implications for the evolution of the Hox class genes of arthropods

Here we report on a partial screen for Hox gene sequences from the geophilomorph centipede Pachymerium ferrugineum, resulting in 11 different sequences. All of these sequences could be homologized to specific Drosophila genes, yielding two representatives for the Dfd class and one each for the remaining classes. Phylogenetic analysis of these data with a broad sample of arthropod/onychophoran homologous sequences confirmed these results and provided further support for the monophyly of the Hox3/zen class. Conversely, the phylogenetic status of ftz-type genes remains uncertain. Our results complement the previous partial findings for two other centipedes (the scolopendromorph Ethmostigmus rubripes and the lithobiomorph Lithobius forficatus) and confirm the expectation that in myriapods, too, all Hox genes classes are present. This suggests that even the Chilopoda, with uniform trunk segments, have the same number of Hox genes as the more tagmatized Insecta.

Functional equivalence of Hox gene products in the specification of the tritocerebrum during embryonic brain development of Drosophila

Hox genes encode evolutionarily conserved transcription factors involved in the specification of segmental identity during embryonic development. This specification of identity is thought to be directed by differential Hox gene action, based on differential spatiotemporal expression patterns, protein sequence differences, interactions with co-factors and regulation of specific downstream genes. During embryonic development of the Drosophila brain, the Hox gene labial is required for the regionalized specification of the tritocerebral neuromere; in the absence of labial, the cells in this brain region do not acquire a neuronal identity and major axonal pathfinding deficits result. We have used genetic rescue experiments to investigate the functional equivalence of the Drosophila Hox gene products in the specification of the tritocerebral neuromere. Using the Gal4-UAS system, we first demonstrate that the labial mutant brain phenotype can be rescued by targeted expression of the Labial protein under the control of CNS-specific labial regulatory elements. We then show that under the control of these CNS-specific regulatory elements, all other Drosophila Hox gene products, except Abdominal-B, are able to efficiently replace Labial in the specification of the tritocerebral neuromere. We also observe a correlation between the rescue efficiency of the Hox proteins and the chromosomal arrangement of their encoding loci. Our results indicate that, despite considerably diverged sequences, most Hox proteins are functionally equivalent in their ability to replace Labial in the specification of neuronal identity. This suggests that in embryonic brain development, differences in Hox gene action rely mainly on cis-acting regulatory elements and not on Hox protein specificity.

Evolution of the echinoderm Hox gene cluster

Extant echinoderms are members of an ancient and highly derived deuterostome phylum. The composition and arrangement of their Hox gene clusters are consequently of interest not only from the perspective of evolution of development, but also in terms of metazoan phylogeny and body plan evolution. Over the last decade numerous workers have reported partial Hox gene sequences from a variety of echinoderms. In this paper we used a combined methods approach to analyze phylogenetic relationships between 68 echinoderm Hox homeodomain fragments, from species of five extant classes--two asteroids, one crinoid, one ophiuroid, one holothuroid, and three echinoids. This analysis strengthens Mito and Endo's (2000) proposition that the ancestral echinoderm's Hox gene cluster contained at least eleven genes, including at least four posterior paralogous group genes. However, representatives of all paralogous groups are not known from all echinoderm classes. In particular, these data suggest that echinoids may have lost a posterior group Hox gene subsequent to the divergence of the echinoderm classes. Evolution of the highly derived echinoderm body plan may have been accompanied by class-specific duplication, diversification and loss of Hox genes.

Conservation of Hox/ParaHox-related genes in the early development of a cnidarian

To clarify the relationship between axial patterning in cnidarians and bilaterians, we have investigated the embryonic development of the hydrozoan Podocoryne carnea. The expression of Hox-like homeobox genes was analyzed by RT-PCR and in situ hybridization. Cnox1-Pc, an anterior Hox gene, is a maternal message. It is present throughout larval development, first weakly in all blastomeres and later restricted mostly to the anterior pole of the planula. Gsx, an anterior ParaHox gene, is first seen in the anterior endoderm but also extends into posterior regions. Cnox4-Pc, an orphan Hox-like gene, is expressed in the egg as a ring-shaped cloud around the germinal vesicle. After fertilization, the message remains in most animal blastomeres. When the embryo elongates in late blastula, staining is restricted to a few cells at the posterior pole where gastrulation will start. However, once gastrulation starts, the Cnox4-Pc signal disappears and is absent in later stages of larval development. Phylogenetic analysis shows that not all cnidarian Hox-like genes have recognizable orthologues in bilaterian groups. However, the expression analysis of Cnox1-Pc and Gsx correlates to some extent with the expression pattern of cognate genes of bilaterians, confirming the conservation of genes involved in organizing animal body plans and their putative common ancestral origin.

Hoxd10 induction and regionalization in the developing lumbosacral spinal cord

We have used Hoxd10 expression as a primary marker of the lumbosacral region to examine the early programming of regional characteristics within the posterior spinal cord of the chick embryo. Hoxd10 is uniquely expressed at a high level in the lumbosacral cord, from the earliest stages of motor column formation through stages of motoneuron axon outgrowth. To define the time period when this gene pattern is determined, we assessed Hoxd10 expression after transposition of lumbosacral and thoracic segments at early neural tube stages. We present evidence that there is an early prepattern for Hoxd10 expression in the lumbosacral neural tube; a prepattern that is established at or before stages of neural tube closure. Cells within more posterior lumbosacral segments have a greater ability to develop high level Hoxd10 expression than the most anterior lumbosacral segments or thoracic segments. During subsequent neural tube stages, this prepattern is amplified and stabilized by environmental signals such that all lumbosacral segments acquire the ability to develop high levels of Hoxd10, independent of their axial environment. Results from experiments in which posterior neural segments and/or paraxial mesoderm segments were placed at different axial levels suggest that signals setting Hoxd10 expression form a decreasing posterior-to-anterior gradient. Our experiments do not, however, implicate adjacent paraxial mesoderm as the only source of graded signals. We suggest, instead, that signals from more posterior embryonic regions influence Hoxd10 expression after the early establishment of a regional prepattern. Concurrent analyses of patterns of LIM proteins and motor column organization after experimental surgeries suggest that the programming of these characteristics follows similar rules.

Characterization of the Hox gene cluster in the malaria vector mosquito, Anopheles gambiae

The Hox genes play a central role in regulating development and are involved in the specification of cell fates along the anteroposterior axis. In insects and vertebrates, these genes are clustered and organized in an arrangement that is largely conserved across evolutionary lineages. By exploiting the sequence conservation of the homeobox, orthologues of the Hox genes Sex combs reduced (Scr), fushi tarazu (ftz), Antennapedia (Antp), Ultrabithorax (Ubx), and abdominal-A (abd-A) have been isolated from the malaria vector mosquito, Anopheles gambiae. These genes were first identified in Drosophila, where they achieve a high level of functional complexity, in part, by the use of alternative promoters, polyadenylation sites, and splicing to generate different protein isoforms. Preliminary analyses of the Anopheles Hox genes suggest that they do not achieve their functional complexity in the same manner. Using a combination of in situ hybridization to polytene chromosomes and chromosome walking, the Anopheles Hox genes have been localized to a single cluster in the region 19D-E on chromosome 2R, a situation distinct from that of Drosophila where the Hox complex is split into two clusters. This study, therefore, provides a framework for future comparative analyses of the structure, organization, and expression of developmental regulatory genes between the lower and higher Diptera. Moreover, the genes that have been isolated enhance the genetic and physical maps of chromosome 2R in this medically important mosquito species.

Evolution of Hoxa-11 in lineages phylogenetically positioned along the fin-limb transition

HOXA11 is a transcription factor implicated in paired appendage development. To identify signatures of evolutionary change in the structural, and putative functional, domains of HOXA11, we studied its evolution in tetrapod and nontetrapod lineages that represent approximately 1.5 billion years of evolutionary time. Here, Hoxa-11 gene proper sequences were determined for frog (Xenopus tropicalis), coelacanth (Latimeria chalumnae), common zebrafish (Danio rerio; Hoxa-11a and Hoxa-11b paralogs), and giant zebrafish (D. aequipinnatus; Hoxa-11b) and aligned against previously published Hoxa-11 sequences of human, mouse, chick, and newt. Based on aligned Hoxa-11 amino acid sequences, the protein was demarcated into three segments: Domains I (N-terminal) and III (homeobox + C-terminal), which varied slightly in rates and patterns of evolution, and a variable, overall hydrophilic region (HyD), which partially overlaps with Domain I. As judged by character reconstructions of HOXA11 Domains I and III, no significant changes in rates of coding sequence evolution occurred in tetrapods (frog and chick), relative to coelacanth (a lobe-finned fish), i.e., across the fin-limb transition. Accelerated rates of Hoxa-11 coding sequence evolution were observed for the mammalian and newt lineages. This was shown to be a gene-specific phenomenon. The duplicated Hoxa-11a and Hoxa-11b genes of zebrafish exhibited accelerated rates of evolution and accumulated substitutions at sites that are conserved among coelacanth and all tetrapods examined. Amino acid sequence comparisons of the HyD of HOXA11 suggested that a putative repressor subdomain, containing stretches of consecutive alanine residues, emerged within the tetrapods. A high degree of nucleotide conservation in the 5' half of the Hoxa-11 intron was observed for tetrapod and nontetrapod lineages. Using electrophoretic mobility shift assays, a 35-bp intron sequence, which is 100% conserved in all Hoxa-11 loci except for the zebrafish Hoxa-11a paralog, was found to bind protein(s) in HeLa and chick whole-cell extracts.

The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14

The amphioxus (Branchiostoma floridae) Hox cluster is a model for the ancestral vertebrate cluster, prior to the hypothesized genome-wide duplications that may have facilitated the evolution of the vertebrate body plan. Here we describe the posterior (5') genes of the amphioxus cluster, and report the isolation of four new homeobox genes. Vertebrates possess 13 types of Hox gene (paralogy groups), but we show that amphioxus possesses more than 13 Hox genes. Amphioxus is now the first animal in which a Hox14 gene has been found. Our mapping and phylogenetic analysis of amphioxus "Posterior Class" Hox genes reveals that these genes are evolving at a faster rate in deuterostomes than in protostomes, a phenomenon we term Posterior Flexibility.

Characterization of Hoxa-10/Hoxa-11 transheterozygotes reveals functional redundancy and regulatory interactions

Hox genes show related sequences and overlapping expression domains that often reflect functional redundancy as well as a common evolutionary origin. To accurately define their functions, it has become necessary to compare phenotypes of mice with single and multiple Hox gene mutations. Here, we focus on two Abd-B-type genes, Hoxa-10 and Hoxa-11, which are coexpressed in developing vertebrae, limbs, and reproductive tracts. To assess possible functional redundancy between these two genes, Hoxa-10/Hoxa-11 transheterozygotes were produced by genetic intercrosses and analyzed. This compound mutation resulted in synergistic defects in transheterozygous limbs and reproductive tracts, but not in vertebrae. In the forelimb, distal radial/ulnar thickening and pisiform/triangular carpal fusion were observed in 35 and 21% of transheterozygotes, respectively, but were effectively absent in Hoxa-10 and Hoxa-11 +/- forelimbs. In the hindlimb, distal tibial/fibular thickening and loss of tibial/fibular fusion were observed in >80% of transheterozygotes but in no Hoxa-10 or Hoxa-11 +/- hindlimbs, and all transheterozygotes displayed reduced medial patellar sesamoids, compared to modest incidences in Hoxa-10 and Hoxa-11 +/- mutants. Furthermore, while the reproductive tracts of Hoxa-10 and Hoxa-11 single heterozygous mutants of both sexes were primarily unaffected, male transheterozygotes displayed cryptorchidism and abnormal tortuosity of the ductus deferens, and female transheterozygotes exhibited abnormal uterotubal junctions and narrowing of the uterus. In addition we observed that the targeted mutations of Hoxa-10 and Hoxa-11 each affected the expression of the other gene in the developing prevertebra and reproductive tracts. These results provide a measure of the functional redundancy of Hoxa-10 and Hoxa-11 and a deeper understanding of the phenotypes resulting in the single mutants and help elucidate the regulatory interactions between these two genes.

Evolution of Antp-class genes and differential expression of Hydra Hox/paraHox genes in anterior patterning

The conservation of developmental functions exerted by Antp-class homeoproteins in protostomes and deuterostomes suggested that homologs with related functions are present in diploblastic animals. Our phylogenetic analyses showed that Antp-class homeodomains belong either to non-Hox or to Hox/paraHox families. Among the 13 non-Hox families, 9 have diploblastic homologs, Msx, Emx, Barx, Evx, Tlx, NK-2, and Prh/Hex, Not, and Dlx, reported here. Among the Hox/paraHox, poriferan sequences were not found, and the cnidarian sequences formed at least five distinct cnox families. Two are significantly related to the paraHox Gsx (cnox-2) and the mox (cnox-5) sequences, whereas three display some relatedness to the Hox paralog groups 1 (cnox-1), 9/10 (cnox-3) and the paraHox cdx (cnox-4). Intermediate Hox/paraHox genes (PG 3 to 8 and lox) did not have clear cnidarian counterparts. In Hydra, cnox-1, cnox-2, and cnox-3 were not found chromosomally linked within a 150-kb range and displayed specific expression patterns in the adult head. During regeneration, cnox-1 was expressed as an early gene whatever the polarity, whereas cnox-2 was up-regulated later during head but not foot regeneration. Finally, cnox-3 expression was reestablished in the adult head once it was fully formed. These results suggest that the Hydra genes related to anterior Hox/paraHox genes are involved at different stages of apical differentiation. However, the positional information defining the oral/aboral axis in Hydra cannot be correlated strictly to that characterizing the anterior-posterior axis in vertebrates or arthropods.

Colonial origin for Emetazoa: major morphological transitions and the origin of bilaterian complexity

A new hypothesis for the evolution of Bilateria is presented. It is based on a reinterpretation of the morphological characters shared by protostomes and deuterostomes, which, when taken together with developmental processes shared by the two lineages, lead to the inescapable conclusion that the last common ancestor of Bilateria was complex. It possessed a head, a segmented trunk, and a tail. The segmented trunk was further divided into two sections. A dorsal brain innervated one or more sensory cells, which included photoreceptors. "Appendages" or outgrowths were present. The bilaterian ancestor also possessed serially repeated "segments" that were expressed ontogenetically as blocks of mesoderm or somites with adjoining fields of ectoderm or neuroectoderm. It displayed serially repeated gonads (gonocoels), each with a gonoduct and gonopore to the exterior, and serially repeated "coeloms" with connections to both the gut and the exterior (gill slits and pores). Podocytes, some of which were serially repeated in the trunk, formed sites of ultrafiltration. In addition, the bilaterian ancestor had unsegmented coeloms and a contractile blood vessel or "heart" formed by coelomic myoepithelial cells. These cells and their underlying basement membrane confine the hemocoelic fluid, or blood, in the connective tissue compartment. A possible scenario to account for this particular suite of characters is one in which a colony of organisms with a cnidarian grade of organization became individuated into a new entity with a bilaterian grade of organization. The transformation postulated encompassed three major transitions in the evolution of animals. These transitions included the origins of Metazoa, Eumetazoa, and Bilateria and involved the successive development of poriferan, cnidarian, and bilaterian grades of organization. Two models are presented for the sponge-to-cnidarian transition. In both models the loss of a flow-through pattern of water circulation in poriferans and the establishment of a single opening and epithelia sensu stricto in cnidarians are considered crucial events. In the model offered for the cnidarian-to-bilaterian transition, the last common ancestor of Eumetazoa is considered to have had a colonial, cnidarian-grade of organization. The ancestral cnidarian body plan would have been similar to that exhibited by pennatulacean anthozoans. It is postulated that a colonial organization could have provided a preadaptive framework for the evolution of the complex and modularized body plan of the triploblastic ancestor of Bilateria. Thus, one can explore the possibility that problematica such as ctenophores, the Ediacaran biota, archaeocyaths, and Yunnanozoon reflect the fact that complexity originated early and involved the evolution of a macroscopic compartmented ancestor. Bilaterian complexity can be understood in terms of Beklemishev "cycles" of duplication and colony individuation. Two such cycles appear to have transpired in the early evolution of Metazoa. The first gave rise to a multicellular organism with a sponge grade of organization and the second to the modularized ancestor of Bilateria. The latter episode may have been favored by the ecological conditions in the late Proterozoic. Whatever its cause, the individuation of a cnidarian-grade colony furnishes a possible explanation for the rapid diversification of bilaterians in the late Vendian and Cambrian. The creation of a complex yet versatile prototype, which could be rapidly modified by selection into a profusion of body plans, is postulated to have affected the timing, mode, and extent of the "Cambrian explosion." During the radiations, selective loss or simplification may have been as creative a force as innovation. Finally, colony individuation may have been a unique historical event that imprinted the development of bilaterians as the zootype and phylotypic stage. (ABSTRACT TRUNCATED)

Ancient origins of axial patterning genes: Hox genes and ParaHox genes in the Cnidaria

Among the bilaterally symmetrical, triploblastic animals (the Bilateria), a conserved set of developmental regulatory genes are known to function in patterning the anterior-posterior (AP) axis. This set includes the well-studied Hox cluster genes, and the recently described genes of the ParaHox cluster, which is believed to be the evolutionary sister of the Hox cluster (Brooke et al. 1998). The conserved role of these axial patterning genes in animals as diverse as frogs and flies is believed to reflect an underlying homology (i.e., all bilaterians derive from a common ancestor which possessed an AP axis and the developmental mechanisms responsible for patterning the axis). However, the origin and early evolution of Hox genes and ParaHox genes remain obscure. Repeated attempts have been made to reconstruct the early evolution of Hox genes by analyzing data from the triphoblastic animals, the Bilateria (Schubert et al. 1993; Zhang and Nei 1996). A more precise dating of Hox origins has been elusive due to a lack of sufficient information from outgroup taxa such as the phylum Cnidaria (corals, hydras, jellyfishes, and sea anemones). In combination with outgroup taxa, another potential source of information about Hox origins is outgroup genes (e.g., the genes of the ParaHox cluster). In this article, we present cDNA sequences of two Hox-like genes (anthox2 and anthox6) from the sea anemone, Nematostella vectensis. Phylogenetic analysis indicates that anthox2 (= Cnox2) is homologous to the GSX class of ParaHox genes, and anthox6 is homologous to the anterior class of Hox genes. Therefore, the origin of Hox genes and ParaHox genes occurred prior to the evolutionary split between the Cnidaria and the Bilateria and predated the evolution of the anterior-posterior axis of bilaterian animals. Our analysis also suggests that the central Hox class was invented in the bilaterian lineage, subsequent to their split from the Cnidaria.

Hox gene complexity in medaka fish may Be similar to that in pufferfish rather than zebrafish

Changes in number and the genomic organization of Hox genes have played an important role in metazoan body-plan evolution. They make cluster(s), and in vertebrates, each cluster contains different number of Hox genes that have been classified into 13 groups. There are 39 Hox genes in four clusters on different chromosomes in the mammalian genome. In the fish, while 31 Hox genes in four clusters have been identified in pufferfish Fugu rubripes, 47 Hox genes in seven clusters exist in the zebrafish Danio rerio. To estimate the evolutionary origin of Hox organization in ray-finned fishes, we searched for Hox genes in the medaka fish Oryzias latipes, with a taxon thought to be widely separated from those of pufferfish and zebrafish. We synthesized various mixed oligonucleotides that can work as group-specific primers for PCR, then cloned and sequenced amplified fragments. Numbers of Hox genes identified in the present study were 2 for group 1, 2 for group 2, 1 for group 3, 3 for group 4, 6 for groups 5-7, 2 for group 8, 4 for group 9, 3 for group 10, 1 for group 12, and 3 for group 13. The primers specific for group 11 did not function in this study. Thus, at least 27 Hox genes are present in medaka genome, suggesting that the Hox gene complexity of the medaka genome is similar to that of the pufferfish rather than the zebrafish.

Hox genes in brachiopods and priapulids and protostome evolution

Understanding the early evolution of animal body plans requires knowledge both of metazoan phylogeny and of the genetic and developmental changes involved in the emergence of particular forms. Recent 18S ribosomal RNA phylogenies suggest a three-branched tree for the Bilateria comprising the deuterostomes and two great protostome clades, the lophotrochozoans and ecdysozoans. Here, we show that the complement of Hox genes in critical protostome phyla reflects these phylogenetic relationships and reveals the early evolution of developmental regulatory potential in bilaterians. We have identified Hox genes that are shared by subsets of protostome phyla. These include a diverged pair of posterior (Abdominal-B-like) genes in both a brachiopod and a polychaete annelid, which supports the lophotrochozoan assemblage, and a distinct posterior Hox gene shared by a priapulid, a nematode and the arthropods, which supports the ecdysozoan clade. The ancestors of each of these two major protostome lineages had a minimum of eight to ten Hox genes. The major period of Hox gene expansion and diversification thus occurred before the radiation of each of the three great bilaterian clades.

Isolation of Hox genes from the scyphozoan Cassiopeia xamachana: implications for the early evolution of Hox genes

The isolation of Hox genes from two cnidarian groups, the Hydrozoa and Anthozoa, has sparked hypotheses on the early evolution of Hox genes and a conserved role for these genes for defining a main body axis in all metazoan animals. We have isolated the first five Hox genes, Scox-1 to Scox-5, from the third cnidarian class, the Scyphozoa. For all but one gene, we report full-length homeobox plus flanking sequences. Four of the five genes show close relationship to previously reported Cnox-1 genes from Hydrozoa and Anthozoa. One gene, Scox-2, is an unambiguous homologue of Cnox-2 genes known from Hydrozoa, Anthozoa, and also Placozoa. Based on sequence similarity and phylogenetic analyses of the homeobox and homeodomain sequences of known Hox genes from cnidarians, we suggest the presence of at least five distinct Hox gene families in this phylum, and conclude that the last common ancestor of the Recent cnidarian classes likely possessed a set of Hox genes representing three different families, the Cnox-1, Cnox-2, and Cnox-5 families. The data presented are consistent with the idea that multiple duplication events of genes have occurred within one family at the expense of conservation of the original set of genes, which represent the three ancestral Hox gene families.

Abdominal-B expression in a spider suggests a general role for Abdominal-B in specifying the genital structure

We have cloned an Abdominal-B (Abd-B) orthologue from the spider Cupiennius salei and have analysed its expression pattern during embryogenesis. An early expression domain is seen in the posterior part of the embryo, with an initial border in the third opisthosomal segment and later in the fifth opisthosomal segment. During mid-stage of germ band extension, two additional spots of expression appear in the posterior parts of the limb buds on the second opisthosomal segment. These coincide with the position of the future genital opening and Cs-Abd-B remains expressed in these regions until the openings are formed. In view of the fact that Abd-B and its orthologous genes are also required for specifying the genitalia in Drosophila and vertebrates, we suggest that this function may constitute an independent and ancestral role of Abd-B that can be separated from its role in specifying the posterior part of the body region.

Origin of the metazoan bodyplan: characterization and functional testing of the promoter of the homeobox gene EmH-3 from the freshwater sponge Ephydatia muelleri in mouse 3T3 cells

Porifera [sponges] represent the lowest metazoan phylum, probably already existing prior to the 'Cambrian explosion'. Based on amino acid sequences deduced from cDNAs that code for structural proteins, the monophyly of Metazoa was established. Now we analyzed for the first time a promoter of a sponge gene for its activity in a heterologous cell system from higher Metazoa. The promoter of the homeobox gene EmH-3 was cloned and sequenced from a genomic library of the freshwater sponge Ephydatia muelleri. For the determination of functional promoter activity, transient transfection experiments in mouse NIH 3T3 cells were performed; the promoter was fused with the luciferase reporter gene. The data revealed that a 401 nt long promoter fragment, comprising several binding elements for metazoan transcription factors, showed the highest activity, while the 175 bp long promoter segment, comprising solely the TATA- and Cap boxes, showed only 25% of that activity. This result demonstrates that the sponge promoter is activated by factors present in mammalian cells and supports the view that Porifera, together with the other metazoan phyla, are of monophyletic origin.

The molecular evolution of development

Morphological differences between species, from simple single-character differences to large-scale variation in body plans, can be traced to changes in the timing and location of developmental events. This has led to a growing interest in understanding the genetic basis behind the evolution of developmental systems. Molecular evolutionary genetics provides one of several approaches to dissecting the evolution of developmental systems, by allowing us to reconstruct the history of developmental genetic pathways, infer the origin and diversification of developmental gene functions, and assess the relative contributions of various evolutionary forces in shaping regulatory gene evolution.

Murine Hoxc-9 gene contains a structurally and functionally conserved enhancer

Reporter gene analysis of the Hoxc-9 genomic region in transgenic mice allowed us to identify a positional enhancer in the Hoxc-9 intron that drives expression in the posterior neural tube of midgestation mouse embryos in a Hoxc-9-related manner. Sequence comparison to the chicken Choxc-9 intron revealed the existence of two highly conserved sequence elements (CSEs) in a similar spatial arrangement. These structural similarities in the mammalian and avian lineage are mirrored by conserved function of the chicken Choxc-9 intron in transgenic mice. Deletion analysis of the two introns suggests that full activity of both enhancers depends on cooperation between the two CSEs located close to the respective 5' and 3' splice sites. Following the paradigm of phylogenetically conserved developmental control mechanisms, the Hoxc-9 intragenic enhancer was tested in Drosophila. Our data show that the mouse Hoxc-9 enhancer acts in a conserved fashion in transgenic flies, conferring posteriorly restricted reporter gene expression to the developing central nervous system in third instar larvae. This finding indicates that the Hoxc-9 intragenic enhancer is involved in transcriptional regulatory circuits conserved between vertebrates and arthropods.

Homology of Hox genes and the zootype concept in early metazoan evolution

The correct identification of homologous Hox genes within and between diplo- and triploblastic animals is of crucial importance for recent hypotheses on the anagenetic evolution of animal bauplans. While the homology discussion in general has reached new heights, we apply traditional homology criteria to assign homology to Hox genes from diploblastic animals. Comparison of the Trox-2 gene from the presumably most basal metazoan animal, the placozoan Trichoplax adhaerens, to other Hox genes suggests the presence of unambiguous homologs in Hydrozoa and Scyphozoa and the absence of any specific homolog in triploblasts. Furthermore, the comparisons provide support for the idea that Hox genes-at least in diploblastic animals-are composed of functional subunits (modules), which to some degree have undergone independent evolution. The findings are not readily compatible with the existence of the "zootype" in diploblastic animals.

The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster

Genes of the Hox cluster are restricted to the animal kingdom and play a central role in axial patterning in divergent animal phyla. Despite its evolutionary and developmental significance, the origin of the Hox gene cluster is obscure. The consensus is that a primordial Hox cluster arose by tandem gene duplication close to animal origins. Several homeobox genes with high sequence identity to Hox genes are found outside the Hox cluster and are known as 'dispersed' Hox-like genes; these genes may have been transposed away from an expanding cluster. Here we show that three of these dispersed homeobox genes form a novel gene cluster in the cephalochordate amphioxus. We argue that this 'ParaHox' gene cluster is an ancient paralogue (evolutionary sister) of the Hox gene cluster; the two gene clusters arose by duplication of a ProtoHox gene cluster. Furthermore, we show that amphioxus ParaHox genes have co-linear developmental expression patterns in anterior, middle and posterior tissues. We propose that the origin of distinct Hox and ParaHox genes by gene-cluster duplication facilitated an increase in body complexity during the Cambrian explosion.